Crystal structure and Hirshfeld surface analysis of 1,6-diamino-2-oxo-4-(thiophen-2-yl)-1,2-dihydropyridine-3,5-dicarbonitrile

In the crystal, molecules are linked by intermolecular N—H⋯O and N—H⋯N hydrogen bonds into ribbons parallel to (022) along the a axis. These ribbons are connected by N—H⋯O, N—H⋯N hydrogen bonds and van der Waals interactions.


Chemical context
The various C-C and C-N bond-formation techniques play key roles in organic synthesis (Celik et al., 2023;Chalkha et al., 2023;Tapera et al., 2022;Lakhrissi et al., 2022). The dihydropyridine moiety, comprising heterocycles, demonstrates a wide spectrum of biological activities, such as antitumor, antitubercular, antimicrobial and anti-diabetic (Mohamed et al., 2013;Soliman et al., 2014). On the other hand, a dihydropyridine scaffold is the active structural unit of a variety of natural products, drugs and functional materials. These compounds have found synthetic applications in the construction of many pharmacologically relevant natural alkaloids, such as the isoquinuclidines, ibogaine, mearsine, dioscorine, caldaphinidine D, catharanthine, vinblastine and vincristine (Sharma & Singh, 2017).

Structural commentary
As seen in Fig. 1, the asymmetric unit of the title compound contains two independent molecules (1 and 2). The thiophene ring (S2 0 /C19/C20 0 -C22 0 ) in molecule 2 is rotationally disordered (flip disorder) by ca 180 (around the single C15-C19 bond to which it is attached) over two sites with the siteoccupation factors of 0.9 and 0.1 (fixed after refinement cycles). These two orientations of the thiophene ring in molecule 2 are not equivalent.

Supramolecular features and Hirshfeld surface analysis
In the crystal, molecules are linked by intermolecular N-HÁ Á ÁO and N-HÁ Á ÁN hydrogen bonds into ribbons parallel to (022) along the a-axis ( View of the two independent molecules,1 and 2, in the asymmetric unit of the title compound, with displacement ellipsoids for the non-hydrogen atoms drawn at the 30% probability level. For clarity, the minor disordered components in 2 are omitted.

Figure 2
A view of the intermolecular N-HÁ Á ÁO and N-HÁ Á ÁN interactions along the a axis in the crystal structure of the title compound. For clarity, H atoms not involved in hydrogen bonding and disordered components in 2 are omitted.

Figure 3
A view of the intermolecular N-HÁ Á ÁO and N-HÁ Á ÁN interactions along the b axis in the crystal structure of the title compound. For clarity, H atoms not involved in hydrogen bonding and disordered components in 2 are omitted.

Synthesis and crystallization
The title compound was synthesized using a recently reported procedure (Babaee et al., 2020), and colorless crystals were obtained upon recrystallization from an ethanol/water (3:1) solution at room temperature.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3. The aromatic H atoms were placed at calculated positions (C-H = 0.95 Å ) and refined as riding with U iso (H) = 1.2U eq (C). The N-bound H atoms were found in a difference-Fourier map, and refined freely [N2-H2A = 0.85 (3) (2) and N10-H10B = 0.84 (3) Å ], with U iso (H) = 1.2U eq (N). The thiophene ring (S2/C19-C22) in molecule 2 is rotationally disordered (flip disorder) by ca 180 (around the single C15-C19 bond, to which it is attached) over two sites with the site-occupation factors of 0.9 and 0.1 (fixed after refinement cycles). A DFIX instruction was applied to constrain the distances in the thiophene rings of disordered molecule 2. For these rings, FLAT and EADP instructions were also used.   SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2020).

Special details
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.